Contacts of the helix formed by residues 533 - 547 (chain A) in PDB entry 5AM8
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with SER 533 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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304A LEU* 3.4 11.5 - - - +
519A ALA* 3.0 38.2 + - - +
530A ILE* 2.9 18.0 + - - -
531A TYR 3.2 2.3 + - - -
532A ARG* 1.3 75.0 - - - +
534A THR* 1.3 58.7 + - - +
535A LYS* 3.7 4.0 + - - +
536A ALA* 3.1 17.6 + - - -
537A GLY* 3.0 20.3 + - - -
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Residues in contact with THR 534 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303A SER 4.2 7.2 - - - +
304A LEU 4.4 7.4 - - - +
305A GLU* 3.6 42.2 - - + +
532A ARG 3.3 11.4 + - - +
533A SER* 1.3 70.7 - - - +
535A LYS* 1.3 63.7 + - - +
537A GLY* 3.7 1.4 - - - +
538A ALA* 3.0 27.4 + - - +
541A ARG* 5.3 1.0 + - - -
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Residues in contact with LYS 535 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
518A GLU* 3.5 47.3 + - + +
519A ALA* 4.8 10.8 + - - +
520A GLY* 5.6 1.4 - - - +
533A SER* 3.3 3.7 + - - +
534A THR* 1.3 80.8 + - - +
536A ALA* 1.3 64.8 + - - +
538A ALA* 3.3 7.6 + - - +
539A LYS* 3.2 17.7 + - - +
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Residues in contact with ALA 536 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304A LEU* 4.8 2.0 - - + -
515A LEU* 3.2 41.0 - - + +
518A GLU* 4.2 7.7 - - - +
519A ALA* 4.2 0.9 - - + -
530A ILE* 4.3 17.0 - - + -
533A SER* 3.1 29.5 + - - +
535A LYS* 1.3 75.6 - - - +
537A GLY* 1.3 62.4 + - - +
539A LYS 3.3 1.6 + - - -
540A LEU* 3.0 20.0 + - - +
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Residues in contact with GLY 537 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304A LEU* 3.3 34.7 - - - +
306A LEU* 3.8 3.9 - - - +
533A SER 3.0 10.9 + - - -
534A THR 3.5 0.9 + - - -
535A LYS 3.2 0.2 - - - -
536A ALA* 1.3 77.4 - - - +
538A ALA* 1.3 50.3 + - - +
540A LEU* 3.4 6.2 + - - +
541A ARG* 2.7 43.5 + - - +
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Residues in contact with ALA 538 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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534A THR 3.0 18.0 + - - +
535A LYS* 3.7 8.1 - - - +
536A ALA 3.3 0.2 - - - -
537A GLY* 1.3 74.4 - - - +
539A LYS* 1.3 62.8 + - - +
541A ARG* 3.4 22.4 + - - +
542A LYS* 3.0 29.5 + - - +
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Residues in contact with LYS 539 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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514A ALA* 4.3 11.0 - - - +
515A LEU* 4.0 13.9 - - + -
518A GLU* 3.7 39.6 + - + -
535A LYS 3.2 12.2 + - - +
536A ALA 3.5 8.1 - - - +
537A GLY 3.2 0.2 - - - -
538A ALA* 1.3 78.4 - - - +
540A LEU* 1.3 62.0 + - - +
542A LYS* 3.4 34.1 + - - +
543A VAL* 3.6 10.4 + - - +
558A ASP 3.9 11.1 + - - -
559A MET* 2.7 41.1 + - + +
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Residues in contact with LEU 540 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304A LEU* 4.7 5.6 - - + -
306A LEU* 3.9 21.1 - - + -
391A ILE* 4.3 34.5 - - + +
394A VAL* 5.8 2.0 - - + -
395A LEU* 4.0 24.5 - - + -
511A PHE* 5.4 3.4 - - + -
515A LEU* 4.0 19.0 - - + +
530A ILE* 5.7 0.4 - - + -
536A ALA 3.0 15.7 + - - +
537A GLY* 3.7 4.9 - - - +
539A LYS* 1.3 72.8 - - - +
541A ARG* 1.3 66.0 + - - +
543A VAL* 3.0 21.5 + - + +
544A LEU* 3.1 26.0 + - + +
559A MET* 4.3 16.6 - - + -
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Residues in contact with ARG 541 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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304A LEU 3.9 4.4 + - - -
305A GLU* 3.2 36.3 + - - +
306A LEU* 3.7 20.9 - - + +
371A GLN* 3.6 26.7 - - - +
534A THR 5.3 0.8 + - - -
537A GLY 2.7 40.7 + - - +
538A ALA* 3.5 17.3 - - - +
540A LEU* 1.3 73.8 - - - +
542A LYS* 1.3 62.6 + - + +
544A LEU* 3.2 4.7 + - - +
545A ARG* 2.9 39.0 + - - +
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Residues in contact with LYS 542 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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538A ALA* 3.0 18.4 + - - +
539A LYS* 3.5 32.1 + - - +
540A LEU 3.2 0.2 - - - -
541A ARG* 1.3 76.7 - - - +
543A VAL* 1.3 64.3 + - + +
545A ARG* 4.2 4.6 - - - +
546A ALA* 3.5 18.2 + - - +
550A ARG* 5.3 4.3 + - - +
555A VAL* 5.5 0.6 - - - +
558A ASP* 5.1 12.5 + - - +
559A MET* 6.1 0.2 - - - +
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Residues in contact with VAL 543 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368A TYR* 4.0 11.6 + - + +
383A ALA* 5.9 0.3 - - - +
387A PHE* 3.7 34.1 - - + -
391A ILE* 5.0 6.1 - - + -
511A PHE* 5.1 1.1 - - + -
539A LYS 3.6 8.9 + - - +
540A LEU* 3.0 11.1 + - + +
542A LYS* 1.3 77.0 - - + +
544A LEU* 1.3 68.2 + - + +
546A ALA* 3.0 18.2 + - - +
547A GLY 3.9 3.3 + - - +
555A VAL* 4.1 17.9 - - + +
559A MET* 3.7 44.9 - - + -
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Residues in contact with LEU 544 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306A LEU* 4.4 11.4 - - + -
367A GLN* 3.9 20.9 - - + +
368A TYR* 3.4 40.2 - - + -
371A GLN* 3.7 32.8 - - + +
372A TYR* 3.7 9.0 - - - +
391A ILE* 3.6 39.3 - - + -
540A LEU* 3.1 28.1 + - + +
541A ARG* 3.8 3.4 - - - +
543A VAL* 1.3 75.5 - - + +
545A ARG* 1.3 62.4 + - - +
546A ALA 3.2 1.0 + - - -
547A GLY 3.3 9.4 + - - -
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Residues in contact with ARG 545 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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370A LEU 4.9 1.8 + - - -
371A GLN* 3.1 60.2 + - - +
372A TYR* 4.4 1.8 - - - +
374A ASP* 4.9 14.6 + - - +
375A LEU* 3.8 18.9 - - - +
541A ARG* 2.9 34.1 + - - +
542A LYS* 4.2 4.7 - - - +
543A VAL 3.3 0.2 - - - -
544A LEU* 1.3 75.5 - - - +
546A ALA* 1.3 59.7 + - - +
547A GLY 3.3 0.6 + - - -
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Residues in contact with ALA 546 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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375A LEU* 3.7 3.5 - - - +
542A LYS 3.5 11.7 + - - +
543A VAL* 3.0 15.0 + - - +
545A ARG* 1.3 78.7 - - - +
547A GLY* 1.3 66.1 + - - +
549A SER* 2.6 37.5 + - - +
550A ARG* 4.5 20.6 - - + +
555A VAL* 4.5 14.8 - - + -
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Residues in contact with GLY 547 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368A TYR* 4.4 3.6 + - - -
372A TYR* 3.6 15.0 - - - -
375A LEU* 4.0 3.4 - - - -
379A LEU 3.6 9.2 - - - -
381A ARG 3.0 19.3 - - - -
383A ALA* 3.4 23.6 + - - +
543A VAL 3.9 2.7 + - - +
544A LEU 3.3 7.5 + - - -
545A ARG 3.3 1.4 - - - -
546A ALA* 1.3 79.6 - - - +
548A SER* 1.3 58.2 + - - -
549A SER 3.8 0.2 + - - -
550A ARG 5.1 1.2 + - - +
555A VAL* 5.6 0.3 - - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il